Colombian Indians in the country's southwestern Cauca province will put three leftist rebels on trial after they were captured with explosives and automatic rifles on their territory, while indigenous authorities are resuming talks with a government delegation aimed at ending two weeks of unrest in the troubled region.

Local Indians have risen up against government troops and leftist Farc guerrillas in what they claim is their territory in the northern part of the province. There were several flashpoints on Wednesday:

• Riot police used teargas to drive Indians from a hill in the town of Toribio, which the community had overrun after capturing a small group of soldiers from their hilltop post. Dramatic images of the soldiers being dragged away were splashed across newspapers nationwide.

• Soldiers shot and killed a man when he ignored orders to stop at a nearby military roadblock. Although the victim was not an Indian, it angered a group of Nasa people in the town of Caldono who captured and held 30 soldiers all day before releasing them to a humanitarian organisation.

• Nasa's Indigenous Guard, a group of Indians who aim to maintain order in their territory armed with wooden sticks, detained Farc members who were in possession of explosives, three automatic rifles, two pistols and a ramp to launch homemade mortars.

Feliciano Valencia, a Nasa leader, told the Guardian by telephone from Toribio: "The community, in a public, traditional trial will decide what to do with them."

The Nasa people say they reject the presence of any armed groups in their territory and have given the rebels and the military deadlines to leave. The Indian mobilisations began after a spate of Farc attacks on Toribio and other towns in the region and combat with government troops.

On 11 July, the Farc claimed to have shot down a fighter plane in nearby Jambalo and the Indigenous Guard says it recovered the black box.

The government has rejected any possibility of a troop pullout. Instead, from Friday, it is reorganising military forces in the region so they operate as a joint command with 5,000 troops for three southwestern provinces affected by leftist rebels, drug traffickers and paramilitaries.

Towns and settlements in the north of Cauca province, a historic Farc stronghold, have lived in the crossfire for decades., but the military has stepped up its presence in the region in recent months.

President Juan Manuel Santos said the recent mobilisations were a response to the infiltration of the indigenous groups by the Farc. Quoting from a message he said was found on the computer of a regional Farc leader known as Pacho Chino, Santos told reporters the guerrillas ordered "spreading propaganda in the towns of northern Cauca so the people demand the withdrawal of populated areas".

"This speaks for itself," Santos said, adding that he did not mean to imply that the entire indigenous community was in cahoots with the Farc but "there are elements where we know there are direct links".

Valencia rejected the accusation and said the government uses the same argument whenever the Nasa try to assert their control of the territory.

Cauca is a critical region for the rebels and criminal syndicates such as the Rastrojos as it lies in a corridor between areas where coca – the raw material used in making cocaine – is grown and the Pacific coast where cocaine is shipped to market.

The situation in Cauca has put Santos on the defensive politically. His government's reaction to the mobilisation has come under fire from critics, including former president Alvaro Uribe, who once supported Santos. They complain that the country has seen an erosion in security gains since Santos took power in 2010.